Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 351443 BT1915 pyruvate carboxylase subunit A (NCBI ptt file)
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__Btheta:351443 Length = 503 Score = 453 bits (1166), Expect = e-132 Identities = 231/492 (46%), Positives = 329/492 (66%), Gaps = 5/492 (1%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 M K+L+ANRGEIA RV+R+ R+M I ++A++S+ADR A+HV ADE++ +G +A SY Sbjct: 1 MIKKILVANRGEIAIRVMRSCREMEITSIAIFSEADRTAKHVLYADEAYCVGPAASKESY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L E II++AK+C A+AIHPGYGFLSENA FAR C+ I F+GP + ++AMG K +A+ Sbjct: 61 LNIEKIIEVAKECHADAIHPGYGFLSENATFARRCQEENIIFIGPDPETMEAMGDKISAR 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 + M +AGVP+VPG + +S + KIGYP+++KA+ GGGGKGMR++ S E++ A Sbjct: 121 IKMIEAGVPVVPGTQENLKSVEEAVELCNKIGYPVMLKASMGGGGKGMRLIHSAEEVEEA 180 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 +A+ E+ SSFG+D + +E+++ +P H+E Q+ D GN ++L +R+CS+QRR+QK+VE Sbjct: 181 YTTAKSESLSSFGDDTVYLEKFVEEPHHIEFQILGDKHGNVIHLCERECSVQRRNQKIVE 240 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 E P+ + LRK MGE AVAAAKA++Y GAGT+EFL+D +++F+EMNTRLQVEHP+T Sbjct: 241 ETPSVFVTPELRKDMGEKAVAAAKAVNYIGAGTIEFLVDKHRNYYFLEMNTRLQVEHPIT 300 Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 E V G DLVK Q+ VA G L L+Q +IQ GHA E RI AED F+P+ G + + E Sbjct: 301 EEVVGVDLVKEQIKVADGQVLQLKQKDIQQRGHAIECRICAEDTEMNFMPSPGIIKQITE 360 Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420 P VRIDS V E I YYDPMI KLIVW +R A+ R+ R L +Y++ G+K+NI Sbjct: 361 PN-GIGVRIDSYVYEGYEIPIYYDPMIGKLIVWATNREYAIERMRRVLHEYKLTGVKNNI 419 Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGD----ALIGDSRDEADTAFVLAVLTQLRLREAVS 476 +L I + P F + ++ T FI + G+ ++ S + A + A + L E Sbjct: 420 SYLRAIMDTPDFVEGHYDTGFITKNGEHLQQCIMRTSERAENIAMIAAYMDYLMNLEENR 479 Query: 477 QDVAGHDPFSPW 488 D + P S W Sbjct: 480 GDATDNRPISKW 491 Lambda K H 0.317 0.134 0.380 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 784 Number of extensions: 35 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 673 Length of database: 503 Length adjustment: 36 Effective length of query: 637 Effective length of database: 467 Effective search space: 297479 Effective search space used: 297479 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory